Use the story of the Jedi Academy Trilogy first, then use Exar Kun's spirit to drag out the story of the Great Sith War and tell the story of two different eras, and the main focus could be the Great Sith War. This could make the big three show up and play some role, but the main focus would still be new characters and new saga of another era.

It was 11 ABY in the book but it shouldn't be too much of a problem to push it to 30-40 ABY.